Fortunately the package designer allows you to modify the template file it uses for generating this file. So open up the package designer, switch to the “Manifest” tab and add the assembly reference in the template yourself, but this time, include the SafeControl entry:

You can safely use the SharePoint project tokens in there as well, but only for the SafeControl entry. When you put it into the Assembly entry, the package generator won’t understand it and will add another assembly reference for the project output: